Why Your Gut Is Making You Anxious: The Gut-Brain Connection Nobody Is Talking About

Why Your Gut Is Making You Anxious: The Gut-Brain Connection Nobody's Talking About

By Dr. Matt Altman, MD | Rooted Health Clinic, Central Texas

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Here's a pattern I see almost every day. Someone walks in for anxiety. They've already been to their primary care doctor, already tried an SSRI — maybe two or three. They're still anxious. The next move is usually a benzo or a psychiatry referral for yet another medication adjustment.

And nobody along the way has asked about their digestion.

In my practice, roughly two-thirds of my patient encounters involve GI issues. Anxiety or mood concerns come up in about three-quarters. And here's the part that matters — these aren't two separate groups of people. There's massive overlap. The anxious patients have gut problems. The gut patients have anxiety. Same patients.

This isn't a coincidence. It's biology. And once you understand the mechanism, you can't unsee it.

Your Gut Has Its Own Nervous System

So let's start with the basics. Your GI tract contains roughly 500 million neurons — more than your spinal cord. This enteric nervous system operates semi-independently from your brain, but it's in constant communication through the vagus nerve, which runs from your brainstem all the way down to your gut.

Here's the thing most people don't realize: about 80% of vagal nerve fibers are afferent, meaning they carry information FROM the gut TO the brain. Not the other way around. Your gut is telling your brain how to feel far more than your brain is telling your gut what to do.

That reframes everything. If you're treating anxiety as purely a brain problem, you're ignoring the organ that's sending 80% of the signal.

Where Your Neurotransmitters Actually Come From

This is where it gets really interesting. You have roughly 39 trillion bacteria living in your gut, and they're not just hanging out. They're metabolically active — producing neurotransmitters, short-chain fatty acids, and immune signaling molecules that directly affect how your brain works.

Take serotonin. About 90-95% of your body's serotonin is produced in the gut, not the brain. So when we give someone an SSRI — a selective serotonin reuptake inhibitor — we're trying to increase serotonin signaling in the brain. But we're completely ignoring the fact that the gut, where the vast majority of serotonin is actually made, might be the real problem.

Then there's GABA — your brain's primary calming neurotransmitter. Certain Lactobacillus and Bifidobacterium species directly produce GABA. If your gut bacteria are depleted from antibiotics, poor diet, chronic stress — your GABA production drops. Low GABA means more anxiety. It's that direct.

And when gut bacteria ferment fiber, they produce short-chain fatty acids like butyrate. Butyrate maintains your gut barrier, reduces inflammation, and has direct neuroprotective effects. It's been shown to have antidepressant-like properties in animal models. The cool part is that you can actually increase butyrate production just by feeding the right bacteria — through prebiotic fiber in your diet.

How Gut Inflammation Drives Anxiety

So here's the mechanism that ties it all together, and it's the one most conventional doctors are completely missing.

It starts with gut barrier breakdown. Poor diet, chronic stress, bacterial imbalance, food sensitivities, infections — all of these damage the intestinal lining. The tight junctions between your gut cells loosen up. This is what we call increased intestinal permeability. Some people call it "leaky gut," and I know that term gets eye-rolls from some physicians. The research supporting it doesn't care about their eye-rolls.

Once that barrier is compromised, bacterial fragments — particularly something called lipopolysaccharide, or LPS — leak into the bloodstream. Your immune system recognizes LPS as a threat and mounts an inflammatory response. Pro-inflammatory cytokines surge — things like IL-6, TNF-alpha, IL-1beta. These are your body's alarm signals.

Now here's where it becomes a brain problem. Those inflammatory cytokines cross the blood-brain barrier. They activate microglia — the immune cells in your brain — which produce even more inflammatory mediators locally. This is neuroinflammation, and it directly disrupts serotonin, dopamine, and GABA pathways. It activates your HPA axis — your stress response system — leading to elevated cortisol.

The result? Anxiety. Depression. Brain fog. Fatigue. Insomnia. The whole constellation that gets labeled "generalized anxiety disorder" and treated with a prescription pad.

The inflammation came from the gut. The anxiety is downstream. And the SSRI isn't addressing any of it.

This Is Tier 1 — The Foundation

The way I think about it, this falls into what I call my Tier 1 framework. Tier 1 is the foundation — gut health, metabolic health including thyroid, and HPA axis function. These are the things that have to be right before anything else matters.

Tier 2 goes deeper — hormones, environmental toxins, chronic infections like Epstein-Barr virus. And Tier 3 is the complex stuff — genetics, structural issues, things like MTHFR variants that affect methylation.

But you don't jump to Tier 2 or 3 without sorting out Tier 1 first. And gut-driven inflammation is Tier 1. It's foundational. When someone comes to me with anxiety and they've got bloating, constipation, acid reflux — I'm not thinking "anxiety medication adjustment." I'm thinking "what's happening in the gut that's driving this?"

Why "Here's an SSRI" Isn't Enough

I want to be clear — I'm not anti-medication. SSRIs help some people. Benzodiazepines have a role in acute situations. I prescribe psychiatric medications when they're appropriate.

But here's what I see over and over: a patient gets put on an SSRI for anxiety. They feel maybe 30% better. They still have digestive issues. They still have brain fog. They still don't feel right. The dose gets increased. A second medication gets added. Side effects stack up. And the fundamental driver — gut-driven systemic inflammation — was never even evaluated.

That's not personalized medicine. That's a conveyor belt.

What I Actually Do When Someone Comes In With Anxiety

The first step is figuring out what's actually happening in the gut. I often run a GI-MAP — it's a DNA-based stool analysis that shows us pathogenic bacteria, parasites, viruses, beneficial bacteria levels, digestive enzyme function, inflammatory markers like calprotectin, and intestinal permeability markers like zonulin. It's a detailed snapshot of the gut ecosystem instead of guessing.

Beyond that, I'm looking at systemic inflammatory markers — hs-CRP, ESR, homocysteine, ferritin. I want to know if gut-driven inflammation has gone systemic, because that's what's driving the neuroinflammation and the anxiety.

From there, the approach depends entirely on the patient. And this is where I need to talk about something most functional medicine practitioners get wrong.

Meeting Patients Where They Are

I have what I call the Pillars of Health — Sleep, Diet, Exercise, Environment, Community, Mental Health, and Hydration. These are the foundations. When all seven are in a good place, people are remarkably resilient. The science behind every one of them is rock-solid.

But here's the thing. Sometimes a patient walks in and they're so depleted — so exhausted, in so much pain, so deep in depression — that they can't realistically make big lifestyle changes. You can't tell someone who can barely get out of bed to start an elimination diet and join a CrossFit gym. That's tone-deaf.

So sometimes you have to jump above the pillars. You have to intervene medically first — get the patient functional enough that they CAN start making lifestyle changes. For chronic fatigue, chronic EBV, Long COVID patients, that might mean starting ivermectin as a first-line treatment. There's real research behind ivermectin for chronic viral infections and Long COVID, and in my practice it's often the first thing I reach for with these patients. LDN — low dose naltrexone — often comes alongside or after that.

Once someone has enough energy to function, THEN we start building out the pillars. Better sleep. Cleaning up the diet — removing inflammatory triggers like processed foods, excess sugar, seed oils. Adding prebiotic fiber to feed the bacteria that produce butyrate and GABA. Prioritizing nutrient-dense foods — wild-caught fish, fermented foods, colorful vegetables.

For the gut specifically, I might add targeted supplementation based on their test results — specific probiotic strains with research backing for anxiety, L-glutamine for gut barrier repair, magnesium glycinate for nervous system support, omega-3s for inflammation, sometimes butyrate supplements directly.

And we address the nervous system. Chronic stress puts people in sympathetic dominance — fight-or-flight — which directly impairs digestive function and perpetuates the cycle. So we work on vagal tone through breathing exercises, cold exposure, even something as simple as gargling or humming. Sleep optimization. Movement — not chronic cardio, but strength training and walking, tailored to where they are physically.

It's not a straight line. It's iterative. You meet the patient where they are and build from there.

The Research Backs This Up

A 2019 meta-analysis in General Psychiatry examined 34 controlled clinical trials and found that probiotic supplementation significantly reduced anxiety symptoms, with even greater effects when combined with dietary changes. A 2022 study in Molecular Psychiatry showed that a psychobiotic diet — emphasizing prebiotic and fermented foods — significantly reduced perceived stress compared to a control diet in just four weeks.

This isn't fringe. This is published in major journals. The gut-brain axis is one of the most actively researched areas in medicine right now, and the data keeps pointing in the same direction: fix the gut, and the brain follows.

What This Means If You're Struggling

If you've been told your anxiety is "just chemical" and you need to adjust your medication — ask about your gut. If you have digestive symptoms alongside your anxiety — bloating, constipation, diarrhea, acid reflux — that's not a coincidence. Your body is trying to tell you something.

I see patients every week who've been stuck in the medication cycle for years. They're not broken. Their brain chemistry isn't irreparably flawed. In many cases, their gut is inflamed, their bacteria are disrupted, and their nervous system is stuck in overdrive.

Fix the gut, calm the inflammation, support the nervous system — and the anxiety starts resolving in ways no SSRI could touch. That's root-cause medicine. That's what we do at Rooted Health.

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References

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